Type 2 diabetes is a complex disorder characterized by multiple metabolic abnormalities and preventable by lifestyle changes. We aimed to identify metabolites associated with glucose metabolism in individuals at risk of type 2 diabetes and those affected by a lifestyle intervention. LC-MS metabolomics was performed on baseline and 1-year samples from 631 individuals at increased risk of type 2 diabetes, categorized into four groups by baseline glucose metabolism. The 1-year samples were from 456 non-diabetic individuals randomized to the intervention. Significant differences in the metabolite signature were observed between baseline glucose metabolism groups, particularly in amino acids, acylcarnitines, and phospholipids. Fatty acid amides, phospholipids, amino acids, DMGV, and 5-AVAB responded most to the lifestyle intervention. Lysophosphatidylcholines containing odd-chain fatty acids showed associations with improved glucose metabolism. Twenty-five metabolites differed between the baseline groups, responded to the intervention, and were associated with changes in glucose metabolism. The findings suggest a metabolite panel could be used in distinguishing individuals with varying degrees of glucose metabolism for early prediction of type 2 diabetes onset. A substantial proportion of these metabolites responded to the lifestyle intervention. These results suggest that metabolites associated with abnormal glucose tolerance potentially reflect responses to personalized interventions.